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Here we argue that the genus Sphagnum (peat moss) represents The Sphagnome Project: enabling an unparalleled model system for ecological and evolutionary , empowered by its contribution to global carbon cycling ecological and evolutionary and emerging genomic resources. Sphagnum species play a major insights through a genus-level role in peatland formation, a prime example of ecosystem engineering, whereby the organism manipulates its surrounding sequencing project habitat. Sphagnum primary production influences carbon and nutrient cycling, such as methane production and soil carbon storage, in many boreal forests and peatlands (Turetsky et al., 2012). Sphagnum ecosystem engineering involves the accumula- Summary tion of peat that facilitates its own growth while making the surrounding environment hostile for vascular plants (van Breemen, Considerable progress has been made in ecological and evolutionary 1995). Ultimately these multi-level processes lead to the formation genetics with studies demonstrating how genes underlying plant of peatlands that occupy nearly 3% of the land surface and store and microbial traits can influence adaptation and even ‘extend’ to 25% of the world’s soil carbon as recalcitrant peat (Yu et al., 2010). influence community structure and ecosystem level processes. The latter point has led to the assertion that Sphagnum has a greater Progress in this area is limited to model systems with deep genetic impact on global carbon fluxes, and therefore climate, than and genomic resources that often have negligible ecological impact any other single genus of plants (Clymo & Hayward, 1982; van or interest. Thus, important linkages between genetic adaptations Breemen, 1995). and their consequences at organismal and ecological scales are often The Sphagnum sequencing project provides a novel nonfood lacking. Here we introduce the Sphagnome Project, which incor- crop or nonbioenergy feedstock example for a plant-based genome porates genomics into a long-running history of Sphagnum research sequencing project aimed specifically at carbon cycling. The project that has documented unparalleled contributions to peatland ecol- is developing resources for within-species genetic associations with ogy, carbon sequestration, biogeochemistry, microbiome research, ecologically relevant functional traits, and the extension of those niche construction, and ecosystem engineering. The Sphagnome gene-to-trait relationships to additional species within the Project encompasses a genus-level sequencing effort that repre- Sphagnum genus. We refer to this effort collectively as the sents a new type of model system driven not only by genetic Sphagnome Project. In the following sections, we provide a brief tractability, but by ecologically relevant questions and hypotheses. introduction to the ecology and of this unique plant genus. We then outline a research roadmap that highlights scientific questions relevant to the disclosure and use of a genus-wide genomic resource for Sphagnum in two major areas of distinct but overlapping research: (1) carbon sequestration and global biogeo- chemistry; and (2) niche construction, ecosystem engineering, and Introduction microbial associations. We demonstrate that the Sphagnome The discovery, characterization, and prediction of genes associated Project is an example of a novel model system aimed at addressing with traits, and how those traits influence ecosystem function, are ecologically relevant questions and hypotheses across levels of key challenges, especially in the face of changing climatic organizations. conditions (Whitham et al., 2006). Climate-driven alteration of biological processes occurs across all levels of organization, and is Sphagnum ecology and evolution expected to impact a wide range of ecosystem goods and services including biodiversity, nutrient cycling, climate feedback regula- Functional traits and ecosystem function tion, and productivity (Rockstr€om et al., 2009). However, our ability to associate genes with traits of ecological interest is generally Sphagnum has a remarkable ability to create and then uniquely restricted to plant model systems primarily developed for crop and thrive in nutrient-poor, acidic, and waterlogged conditions. The bioenergy feedstocks, and further limited by the sheer complexity suite of morphological, physiological, and life history traits that of applying genetic and genomic approaches to multiple species or affect Sphagnum fitness, herein termed functional traits, enable this communities. Yet the need to apply system genetic approaches in ‘ecosystem engineer’ (Jones et al., 1994) to gain a competitive complex communities is paramount as evolution takes place within advantage over other co-occurring species and therefore flourish a complex web of genetic interactions among species (Whitham under relatively harsh environmental conditions. For example, the et al., 2006). ability of Sphagnum to store and transport water is controlled

16 New Phytologist (2018) 217: 16–25 Ó 2017 UT-Battelle www.newphytologist.com New Phytologist Ó 2017 New Phytologist Trust New Phytologist Viewpoints Forum 17 largely by three distinct morphological adaptations – branching the Sphagnum cells die (Hayward & Clymo, 1983). From there architecture, leaf size and arrangement on branches, and hyaline down to the water table the carpet structure is permeable to water cells (Fig. 1a,b; Rydin & Jeglum, 2013). These traits differ and gases (particularly oxygen) and the damp plant substrates begin considerably among species, and are associated with highly to decay in this oxic zone, termed the acrotelm (Ingram, 1978; partitioned microhabitat preferences where Sphagnum species Clymo & Hayward, 1982). The consequent loss of stem strength coexist within a peatland. Hummock-forming species, growing and increasing weight eventually result in collapse of the plant c. > 30 cm above the water table, have small close-set leaves forming structure. This reduces the pore size so water can no longer flow numerous interconnected small capillary spaces (Fig. 1). Spreading easily through it, and from this point downwards the peat is branches allow lateral movement of water through the capillary permanently waterlogged and this is what determines the depth of continuum, while numerous close-set pendant branches appressed the water table. In this waterlogged zone, oxygen is consumed by to the stem form an efficient vertical water-transport system. aerobic respiration more rapidly than it can be replenished by Consequently, Sphagnum species growing on hummocks can wick diffusion (which is 10 000 times slower in water than it is in air), moisture and maintain metabolic activity even during drought creating the anoxic catotelm (Clymo, 1983). Hence, through (Rice & Giles, 1996). In all species, dead hyaline cells in the leaves distinct traits, Sphagnum generates environmental conditions that and the outer cortex of the stems and branches act as water-storage are suitable for its own growth but hostile for the vast majority of structures. other plants (e.g. van Breemen, 1995; Rydin & Jeglum, 2013). The capitula at the top of the stems are alive, but a few (c.5) The mechanisms by which Sphagnum inhibits fungal and microbial centimeters down 99% of the light has been absorbed and most of decomposition – and hence promotes peat accumulation – are not

Fig. 1 Morphological traits of Sphagnum. Left panel, four representative species (modified from Crum, 1984). (a) Plant habits showing differences in branch density. (b) Branch leaf cross-sections showing arrangements of larger hyaline cells. As in most mosses, Sphagnum leaves consist of a single layer of cells, but unlike in other mosses, the leaf cells are dimorphic, comprising large hyaline cells, dead and empty at maturity, alternating with narrow photosynthetic chlorophyllose cells. In some species (e.g. top), those chlorophyllose cells are not exposed at the leaf surface and in other species they are exposed at the inner or outer surface. (c) Surface view of branch leaf cells, showing variously arranged pores on hyaline cells. The chlorphyllose cells are very narrow, forming a network around each hyaline cell. (d) Branch fascicles, each including so-called spreading and pendent branches. (e) Branch leaf. (f) Stem cross-section showing variously developed, sometimes enlarged outer cortex cells. Right panel, one (haploid) gametophyte plant with stalked capsules releasing spores (modified from Weston et al., 2015). Inset, detail of branch leaf cells showing differentiation of chlorophyllose and hyaline cells.

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fully understood, but involve both the external environment 200–300 species, Sphagnum is by far the largest genus in the engineered by the species, as well as the internal of its Sphagnopsida and the most important for peatlands. Sphagnum plant tissue, particularly the low nitrogen : carbon (N : C) ratio (a species share a common ancestor in the late Tertiary, a surprisingly reflection of the unusually efficient use of nitrogen in producing recent radiation considering the great antiquity of Sphagnopsida new biomass) (Bragazza et al., 2006). A passive mechanism for (Shaw et al., 2010). This recent radiation, which may have occurred intrinsic decay resistance in the oxic acrotelm layer is suggested by following the mid-Miocene climatic optimum, coincides with the the correlation of microbial decomposition of Sphagnum litter with rise of boreal peatlands in the Northern Hemisphere (Greb et al., the relative amounts of structural vs metabolic carbohydrates 2006). (Turetsky et al., 2008). Active mechanisms of antimicrobial activity Today, Sphagnum occurs on all continents aside from are also implicated, mainly through acid hydrolysis of cell-wall Antarctica (Crum, 1984). The genus dominates wetland habitats polysaccharides, fragments of which are released into the soil water throughout the boreal zone of the Northern Hemisphere but is as ‘sphagnan’ (Hajek et al., 2011). The precise mechanisms for the also diverse at tropical latitudes, especially in South America (as antimicrobial activity of sphagnan are still under investigation, but well as in tropical Africa and Asia). At tropical latitudes, may involve lowering soil pH, reducing availability of nitrogen and Sphagnum sometimes occurs in high altitude peatlands, but in carbon, or interfering with extracellular enzymes by immobilizing lower altitude tropical regions they typically grow on wet soil them in a polyelectrolyte complex (Hajek et al., 2011). Soluble banks, along streams, and on dripping rocks, and do not phenolic compounds, either leached directly from Sphagnum tissue accumulate substantial amounts of peat. Sphagnum comprises five or produced during its breakdown, may play a more minor role in major subgenera (Fig. 2a; Shaw et al., 2016a). The small tissue preservation, physically protecting polysaccharides through subgenus Rigida (c.2–4 species), sister to the four other the formation of humic substances (Hajek et al., 2011). While subgenera, sometimes occur in peatlands, but its species are environmental factors such as soil oxygen profiles serve as never dominant and are not major peat-formers. Most Sphagnum important regulators of peat decomposition (cf. Freeman et al., species belong to the remaining two clades, both of which include 2001) it is clear that a variety of mechanisms contribute to slow important peat-forming species. The species in one clade decomposition of Sphagnum tissue, thereby retarding the turnover (subgenera Cuspidata + Subsecunda) generally occupy hollows of organic biomass in peatlands and sequestering carbon in the close to or at the water table, whereas those in the other clade form of peat for centuries. (subgenera Sphagnum + Acutifolia) generally create lawns and raised hummocks more distant from the water table (Fig. 2b). For decades, peatland ecologists have noted that individual Sphagnum Phylogeny and evolution species have narrow realized niches along this hydrological Like all mosses, the haploid gametophyte is the dominant life cycle gradient – from low hollow to high hummock (Vitt & Slack, stage for Sphagnum (Fig. 1). Haploid spores germinate into a 1984). Sphagnum species also exhibit narrow preferences along a filamentous protonema, quickly followed by a thalloid protonemal chemical gradient, with some species preferring acidic phase, before transitioning into mature haploid gametophytes. A ombrotrophic bogs and other species preferring fens with more single spore can result in a large clonal biomass through vegetative neutral pH. Unlike preferences along the hydrological gradient, growth. Furthermore, the ability to propagate clonally is ubiqui- species preferences along the chemical gradient do not exhibit a tous in Sphagnum and typical clone sizes vary among species strong phylogenetic signal (Johnson et al., 2015). During the (Cronberg, 1996). In S. austinii, one clone occurs throughout rapid radiation of modern Sphagnum, microhabitat preferences North America and the same dominates in Europe (Kyrkjeeide along the chemical gradient plausibly evolved simultaneously in et al., 2016). A single clone of S. subnitens extends from Oregon to unrelated groups, creating natural experiments with which the the westernmost Aleutian Islands (Karlin et al., 2011). Reproduc- genetic basis of microhabitat preferences can be disentangled tive seasons are species-specific and sperm require water to access from phylogenetic history. the egg cell in the archegonial venter to form the zygote. The formation of the zygote marks the beginning of the brief diploid Developing resources for a tractable Sphagnum model stage of development and at maturity meiosis occurs within the system with evolutionary and ecological relevance capsule, producing haploid spores. Sphagnum is one of four genera in the class Sphagnopsida Genomic resources for Sphagnum are rapidly expanding (phylum Bryophyta: mosses), an ancient lineage of land plants. (https://phytozome.jgi.doe.gov). The Sphagnome Project will Molecular phylogenies suggest the Sphagnopsida diverged from provide two high quality reference genomes (S. magellanicum and other mosses > 250–350 million years ago (mya) (Shaw et al., S. fallax), sequences for 15 additional species across the Sphagnum 2010), and fossils of peat moss-like fragments, which are the oldest phylogeny (Fig. 2), and shallow sequencing of c. 200 individual known land plant macrofossils to date, have been found in the members from a haploid-sib pedigree. A draft genome for S. fallax Ordovician rocks (c. 500 mya, Cardona-Correa et al., 2016). Fossil is now available on https://phytozome.jgi.doe.gov. These Sphag- Sphagnum and close relatives are recognized by the unique cell nome Project resources are motivated by two overarching aims: (1) pattern in leaves. Three of the genera in the Sphagnopsida contain identifying genetic associations with ecologically relevant func- just one or two species each, and none of them form extensive peats tional traits within species; and (2) extending those gene-to-trait nor do they dominate wetlands as do species of Sphagnum. With relationships to additional species within genus.

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(a) (b)

(c)

Fig. 2 Distribution, phylogeny and habitat preference of species within the Sphagnome Project. (a) A recent phylogeny based on Shaw et al. (2016a) with colored branches representing subgenus designations (brown, Rigida; yellow, Subsecunda; green, Cuspidata; blue, Sphagnum; purple, Acutifolia) and colored circles next to species being sequenced with the Sphagnome Project; (b) generalized habitat preferences for Sphagnum species typical of boreal peatlands, in relation to pore water pH and height above water table; (c) global distribution of Sphagnum fallax (green) and Sphagnum magellanicum (blue). Note that Sphagnum affine (Sphagnum), Sphagnum cribrosum (Subsecunda), Sphagnum fimbriatum (Acutifolia) and Sphagnum molle (Acutifolia) are not in the figure because they are not boreal peatland species, but have been sequenced as part of the Sphagnome Project.

haploid siblings in response to laboratory growth conditions, Sphagnum pedigree sequencing and gene-to-trait mapping temperature and pH (Shaw et al., 2016b). Sphagnum is haploid in The Sphagnome Project is producing high-quality reference its dominant life cycle stage, which eliminates the confounding genomes for S. magellanicum Brid. and S. fallax H. Klinggr (Shaw heterozygosity that can mask allele expression. Therefore, the F1 et al., 2016b). These two peat-forming species are in different (gametophytic) generation can be used in trait mapping, which is subgenera, occupy very different microhabitats in boreal peatlands, not possible for genetic studies in diploid nonbryophyte organisms and will provide strong contrasts for investigating phylogenetic and where, at a minimum, a segregating F2 pedigree is required. ecological differences (Fig. 2; Johnson et al., 2015). To fulfill the Furthermore, the paternal genotype can be reconstructed by first aim focusing on within-species variation, the Sphagnome subtracting the progeny genetic markers from the maternal Project will conduct resequencing of c. 200 individuals from a markers. This latter point is especially important, as controlled S. fallax pedigree to generate a high quality genetic linkage map that crosses are currently difficult to perform in Sphagnum. As recently will facilitate gene-to-trait experimental approaches (Fig. 3) and shown in the Sphagnum moss-relative Physcomitrella patens genome assembly. The pedigree was developed from single stem (Stevenson et al., 2016), the simplified genetics of mosses coupled descent propagation using sporelings germinated from a single field with linkage-analysis can provide a powerful means of predicting collected sporophyte; all individuals are haploid sibs. Because S. phenotypes from DNA markers and their underlying causal alleles fallax has separate gametophytic sexes, pedigree individuals can be (Fig. 3). maintained in clonal culture without risk of intra-gametophytic Recent advances in maintaining Sphagnum tissue cultures (Beike selfing. Preliminary data show vast phenotypic variation among et al., 2015) have improved the reliability of producing axenic

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cultures that produce Sphagnum plants that are morphologically similar to field-collected specimens. The Sphagnome Project encompasses a developing germplasm collection that includes culture material for all species being sequenced and a S. fallax haploid-sib pedigree. The low stature of Sphagnum and ease of establishing populations in trans-well culture plates that have relatively small ‘bench top’ space requirements enable rapid phenotyping that is necessary for gene-to-trait studies (Fig. 3). Further, this germplasm collection can be used to test responses of Sphagnum genotypes to different environmental conditions. Because the complete genomes of these genotypes will already be known as a result of resequencing, genetic associations can be made as soon as phenotypic data are collected. Due to the small size of Sphagnum and other mosses, imaging-based phenotyping will be especially useful in this effort. Single images can capture data on hundreds of individuals, entire populations, and mixed commu- nities, simultaneously aiding the linkage of genes to traits. The broader collection of gene-to-trait associations can be integrated in network models to form a systems biology view of the trait combinations and their correlations underlying phenotype expres- sion and adaptation (Chitwood & Topp, 2015).

A genus-wide approach Extending gene-to-trait relationships beyond a single species is necessary for understanding the evolution of ecosystem function in Sphagnum-dominated peatlands. Traits important for ecosystem function differ among species, including productivity and resource acquisition, resource allocation such as production of secondary compounds, and decomposition rates (Bengtsson et al., 2016; Limpens et al., 2017). Therefore, in addition to the intensive within-species resequencing approach described earlier, the Sphag- nome Project includes the sequencing of 31 individuals across 15 species representing the five major clades within Sphagnum (Fig. 2). This information, combined with ongoing and existing transcrip- tome resources (Devos et al., 2016), will provide the basis for genus- level phylogenomics and comparative genomic analyses in Sphagnum (Fig. 3). This approach is especially useful for the majority of traits in Sphagnum where interspecific variation seems to be greater than intraspecific variation (e.g. Bengtsson et al., 2016). Genetic associations will be tested using models that Fig. 3 Schematic of the proposed depth and breadth genetic approaches incorporate phylogenetic comparative methods (e.g. Blomberg & (Fig. 4 legend). In gene-to-trait studies, linkage-based and association mapping are main approaches used to discover (or map) the genetic basis of Garland, 2002; Revell, 2009) to account for phylogenetic distance quantitative phenotypic variation. Both assume that there is variation for the when identifying gene-to-trait relationships. traits of interest within the population being studied. The linkage-based Through this sequencing effort, gene-to-trait relationships of method relies on individuals with known relationships to each other and DNA multiple species will be placed within a broader phylogenomic variants (termed genetic markers) that segregate through the population. landscape thereby identifying evolutionary patterns associated with The genetic marker is ‘linked’ through proximity to the causal loci and they therefore segregate together. Association mapping does not require known microhabitat preferences and functional traits (Figs 2b, 4). While a relationships among individuals within the population, but instead relies on few recent studies have taken a genus-wide approach to genetic historical recombination from many generations of random mating. associations (e.g. Haudry et al., 2013; Novikova et al., 2016; Pease Together these methods constitute the ‘genetic depth’ approach discussed in et al., 2016) the Sphagnome Project encompasses species that co- the text aimed at identifying candidate genes (lower panel) that are then occupy and engineer the same ecosystem. We anticipate that these included in phylogenomic and comparative genome analyses (upper panel). These analyses are simplified by the fact that Sphagnum gametophytes are genus-wide sequences, phenotype data, and comparative gene-to- typically haploid. Two allopolyploid species (S. palustre, S. papillosum) are trait relationships will enable the detection of genes under purifying included to address subsidiary issues related to the evolution of polyploid or positive selection as well as gene family evolution associated with genomes. major ecological and biogeographic shifts.

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Fig. 4 An integrated approach for Sphagnum as a model system linking genetic information on genes underlying functional traits (depth) with phylogenomic analyses (breadth) to large-scale, emergent properties at the level of the ecosystem. Increases in the availability of genomic resources and recent developments of germplasm resources can facilitate collaborative research across multiple disciplines. Understanding the genetic basis of integrated traits will facilitate our understanding of trait-trade-offs, fitness and selection, and response to environmental change.

Facilitating new ecological and evolutionary advantage from a nutrient competition perspective? Further- understanding more, how do these traits extend beyond the organism? For example, do hummock formation traits covary with tissue chemistry and decomposition rates, and how will these What is the biological basis of unique Sphagnum traits or currently adapted trait combinations influence fitness to combinations of traits, and how do these trait combinations changing environmental conditions? In regard to niche engi- extend beyond the organism? neering, is there evidence for an extended phenotype in Tissue chemistry is a noted functional trait for Sphagnum Sphagnum, and if so, what is the unit of selection, and at (Clymo & Hayward, 1982). Polyuronic acids (cell-wall polysac- which level does selection occur (Whitham et al., 2003)? Do charides that form a pectin-like polymer) comprise 10–30% of neighborhood effects, such as the genetic effect of an individual Sphagnum dry mass. They have a high cation exchange capacity on trait values of neighboring individuals influence how (CEC) initially satisfied with H+, which is rapidly exchanged for Sphagnum traits interact with the environment? How important cations in rainwater, thus making the water around the plants is clonality to the extended Sphagnum phenotype? These acidic (Clymo & Hayward, 1982) and make cation nutrients important questions extend into much broader spheres of the unavailable to microbes and other plants (Stalheim et al., 2009). Sphagnome Project (Fig. 4) and general ecological and evolu- However, the question of a possible link between unique tionary theory. organic compounds and niche engineering by Sphagnum remains a matter of active research (Hajek, 2009; Limpens Did adaptation to spatially or temporally varying climate et al., 2017). It has long been speculated that living Sphagnum variation spark Sphagnum species radiations? benefits from peat formed over time through the accumulation of dead Sphagnum biomass (van Breemen, 1995). Should this Genus-wide phylogenetic analyses of geographic ranges support the be viewed as one type of extended phenotype, where the view that the two major peat-forming, crown clades within phenotype of vertically accumulating peat (dead Sphagnum Sphagnum (Acutifolia + Sphagnum; Cuspidata + Subsecunda) material) changes the function of living Sphagnum at the (Fig. 2a,b) originated and first diversified in the Northern Hemi- surface? Sphagnum plants clearly modify their environment in sphere (J. Shaw et al., unpublished). By contrast, phylogenetic several important ways, but how this influences selection on analyses of large seed plant clades that span tropical and Northern future offspring and other recipient organisms is unknown. We Hemisphere ranges usually reveal tropical origins and rare believe that the Sphagnum genomic resource offers one of the expansions into cold northern climates (Jansson et al., 2013). best opportunities to explore these questions and ultimately Sphagnum represents one of a small minority of groups that appear identify the genetic basis for the traits responsible for ecosystem to have initially diversified at northern latitudes and subsequently engineering in Sphagnum. For example, what is the genetic basis extended their ranges into the tropics. Phylogenetic patterns of tissue chemistry traits, and do these traits impart a fitness indicate that southward range expansions were followed by

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evolutionary radiations that gave rise to groups of tropical species What is the role of Sphagnum and its interacting microbiome nested within larger boreal clades. in ecosystem carbon and nitrogen cycling? Moreover, nonboreal radiations occurred in each of the four large subgenera of Sphagnum, providing phylogenetic patterns that Hyaline cells not only play a vital function as water storage can be used as replicated natural experiments to account for shared organs, but also create a novel and safe habitat for a diverse ancestry when investigating the genetic basis of adaptation and the microflora spanning all domains of life (Fig. 1; Bragina et al., evolution of functional traits associated with range expansions. In 2012; Kostka et al., 2016). The Sphagnum-associated microbiome addition to these radiations, a few individual boreal Sphagnum seems to be divided into two broad categories: those that are host species have extended their ranges into tropical habitats, presum- species specific, with specificity maintained across both the ably more recently. Interspecific and intraspecific comparative sporophyte and gametophyte generations (Bragina et al., 2012), analyses can be harnessed to address several questions. What genes, and those that are host species agnostic with environmental gene families, and genomic regions underwent changes associated factors such as pH and nutrient availability explaining much of with range expansions from boreal to tropical climate zones? Are the community structure (Larmola et al., 2014). With a raised the same genomic features associated with intraspecific and with pH, hyaline cells may serve as ‘oases’ for microbes in acidic interspecific range changes across climate zones? Are the same or peatland pore waters. The ecological function of Sphagnum similar genomic changes associated with climate adaptation in symbionts is just beginning to be explored, with evidence different Sphagnum subgenera, associated with independent range pointing to strong linkages with the cycling of both carbon (i.e. changes? Clarifying functional trait and genomic changes associ- methane oxidation) and nitrogen (i.e. nitrogen fixation). For ated with migrations into warmer climates can provide informative example, diazotrophic cyanobacteria were shown to contribute up analogies to how Sphagnum mosses and, perhaps, other plants may to 35% of cellular nitrogen to the Sphagnum host (Berg et al., respond to current climate warming. 2013; Lindo et al., 2013) while methanotrophic bacteria can provide 5–20% of Sphagnum’s CO2 demand through methane oxidation (Raghoebarsing et al., 2005; Kip et al., 2010). What are the factors that limit or facilitate local-scale Together, methanotrophy and N fixation are tightly linked adaptive evolution? 2 and was estimated to provide over one-third of the new nitrogen There has been much interest regarding the importance of input in a coastal peatland (Larmola et al., 2014), although see relative to local adaptation in response to Ho & Bodelier (2015). Therefore, a number of critical questions environmental heterogeneity, and how such responses can ulti- concerning the Sphagnum microbiome remain, for example what mately extend to influence ecosystem function (Miner et al., 2005). are the signaling and communication pathways between The sequenced haploid-sib pedigree coupled with phenotype Sphagnum and its microbiome, and do these interactions screening will provide the resources necessary for quantitative represent true beneficial symbioses. How do protists and genetics to determine the extent to which a phenotypic change has a miroeukayotes influence peatland carbon and nitrogen cycles quantitative genetic basis (see the ‘Developing resources for a (Jassey et al., 2015)? More questions than answers remain, and tractable Sphagnum model system with evolutionary and ecological achieving a comprehensive understanding of the Sphagnum relevance’ section). Plasticity is inferred as the proportion of microbiome will benefit greatly from the application of compar- phenotypic variance not explained by genetics (Meril€a & Hendry, ative and functional genomics to evaluate microbial community 2014). The use of common gardens, especially when established profiles across Sphagnum lineages and environments, and meta- among multiple environments with appropriate replication and transcriptomics to evaluate symbiotic pathways and metabolism. controls, provides a powerful approach to disentangle genetic from plastic contributions to phenotype. The sequenced Sphagnum How do we model Sphagnum genotype-by-environment haploid-sib pedigree and emerging research community surround- interactions? ing the Sphagnome Project make the establishment of common gardens with characterized genotypes a reality. Finally, the The understanding of Sphagnum trait characteristics and the demonstration that allele frequency shifts occur confirms that underlying trait distributions may have evolution has occurred, with the challenge being the need to important implications for modeling biogeochemistry and vege- determine if changes in specific allele frequencies are relevant to the tation dynamics, both within an ecosystem and across regions up to traits and phenomena being investigated. The sequencing of 15 a global scale. However, the Sphagnum trait characterization Sphagnum species and nearly 200 progeny individuals provides an needed to inform these models is lacking for many high-latitude ideal system to determine shared and species-specific components process-based models (Turetsky et al., 2012). Many ecosystem and of the collective genome and relationships that co-occur with regional models have adopted the concept of plant functional types phylogenetic signals. For example, does a gene family expansion (PFTs), where PFTs are defined as groupings of plant species that coincide with the lineage diversification to novel environments? share similar characteristics and roles in ecosystem function. Together with common garden experiments we will begin to However, recent work suggests that parameterization of PFTs with address questions centering on the relative importance of local current trait values may not be valid under future environmental adaptation vs phenotypic plasticity in Sphagnum responses to conditions because trait values and trait–trait relationships may environmental heterogeneity. change under future environmental conditions (van Bodegom

New Phytologist (2018) 217: 16–25 Ó 2017 UT-Battelle www.newphytologist.com New Phytologist Ó 2017 New Phytologist Trust New Phytologist Viewpoints Forum 23 et al., 2012; Scheiter et al., 2013). In this regard, we will benefit G.G. wrote the paper; Z.L., L.R.B., S.K.R., D.T.H., K.A.M.E., from population genomics programs – like the Sphagnome Project E.D., R.J.N., J.E.K., J.B.G., H.R., J.L., E-S.T., A.C., B.W.B., – where population genetics, genomics and phenotype analysis can E.S.E., T.A.O., M.B.N., E.A.L. and R.S.C. conceived of and be used to statistically model genome features (such as single contributed to the ecological, and modeling section; nucleotide polymorphism (SNP) distributions) to trait value H.K.S., P.S., M.J. and B.T.P. developed the evolutionary genetic predictions. The ‘trait values’ are then entered as parameter values sections; J.S., W.M., K.K.U., J-G.C., P.R. and D.J. contributed to in physiological models. An elegant example of this approach was the bioinformatics and quantitative genetics. presented by Reuning et al. (2015), where quantitative trait locus (QTL) analysis was used to genetically parameterize a physiological David J. Weston1,2*, Merritt R. Turetsky3, Matthew G. model to predict transpiration of specific Arabidopsis genotypes. An Johnson4, Gustaf Granath5,Zo€e Lindo6, Lisa R. Belyea7, intriguing question is whether such ‘genome informed’ ecophys- Steven K. Rice8, David T. Hanson9, Katharina A. M. iological models can be used to decipher the mechanisms of local Engelhardt10, Jeremy Schmutz11,12, Ellen Dorrepaal13, adaptation, which provides deeper insights into heritable variation Eugenie S. Euskirchen14, Hans K. Stenøien15, and trait covariances (and trade-offs) responsible for evolutionary Peter Szov€ enyi16, Michelle Jackson17, Bryan T. Piatkowski17, dynamics (Weinig et al., 2014). Wellington Muchero1, Richard J. Norby2,18, Joel E. Kostka19, Jennifer B. Glass19,Hakan Rydin20, Juul Limpens21, 22 23 1 Conclusions Eeva-Stiina Tuittila , Kristian K. Ullrich , Alyssa Carrell , Brian W. Benscoter24, Jin-Gui Chen1, Tobi A. Oke3, The Sphagnome Project seeks to resolve important and general Mats B. Nilsson25, Priya Ranjan26, Daniel Jacobson1, issues in ecology and evolution including: (1) the niche differen- Erik A. Lilleskov27, R. S. Clymo28 and A. Jonathan Shaw17 tiation and co-occurrence of many closely related Sphagnum species within the same wetland habitat; (2) the genetic regulation of the 1Biosciences Division, Oak Ridge National Laboratory, unique chemical traits that define the central role of Sphagnum Oak Ridge, TN 37831, USA; species in engineering those habitats; (3) the importance of 2Climate Change Science Institute, Oak Ridge National Sphagnum in determining biodiversity patterns of other organisms, Laboratory, Oak Ridge, TN 37831, USA; including microbes; and (4) the role of Sphagnum genetics and 3Department of Integrative Biology, University of Guelph, physiology on biogeochemistry and hydrology at ecosystem to Guelph, ON N1G 2W1, Canada; global scales. With new genomic resources already available and 4Department of Biological Sciences, Texas Tech University, growing rapidly, we are poised to utilize the Sphagnum system for Lubbock, TX 79414, USA; linking genomes and phenotypic traits to community assembly, 5Department of Ecology, Swedish University of Agricultural ecosystem function, and evolutionary processes. Moreover, the Sciences, Box 7044, SE-750 07, Uppsala, Sweden; Sphagnum system can provide unique insights into the phyloge- 6Department of Biology, The University of Western Ontario, netic history of genome and trait evolution, and allow predictions London, ON N6A 5B7, Canada; about how these organismal features are likely to respond to future 7School of Geography, Queen Mary University of London, environmental change. London, E1 4NS, UK; 8Department of Biological Sciences, Union College, Schenectady, NY 12308, USA; Acknowledgements 9Department of Biology, University of New Mexico, Albuquerque, The authors thank Drs Stan Wullschleger, Paul Hanson and two NM 87131, USA; anonymous reviewers for comments on the manuscript. Work 10Appalachian Lab, University of Maryland Center of Environ- related to sequencing efforts are supported by the US Department mental Science, Frostburg, MD 21532, USA; of Energy (DOE) Joint Genome Institute by the Office of Science 11HudsonAlpha Institute of Biotechnology, Huntsville, under contract no. DE-AC02-05CH11231; and germplasm AL 35806, USA; establishment and maintenance is supported by the US DOE, 12Department of Energy Joint Genome Institute, Walnut Creek, Office of Science, Office of Biological and Environmental CA 94598, USA; Research, Early Career Research Program. Oak Ridge National 13Climate Impacts Research Center, Department of Ecology Laboratory is managed by UT-Battelle, LLC, for the US DOE and Environmental Science, Umea University, under contract no. DE-AC05-00OR22725. The authors thank the 98107, Abisko, Sweden; National Evolutionary Synthesis Center (NESCent), NSF #EF- 14Institute of Arctic Biology, University of Alaska, Fairbanks, 0905606 and the New Phytologist Trust for sponsoring workshops AK 99775, USA; on the Sphagnome Project. 15NTNU University Museum, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway; 16Department of Systematic and Evolutionary , University Author contributions of Zurich, 8008, Zurich, Switzerland; D.J.W., A.J.S. and M.R.T. conceived the Sphagnome project and 17Department of Biology, Duke University, Durham, solicited community input; D.J.W., A.J.S., M.R.T., M.G.J. and NC 27708, USA;

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